Apple - Disable Mail notifications on a per account basis
This is possible with iOS 6. Under Settings → Notifications → Mail, notifications can be changed or disabled on a per-account basis.
Once you select the account: Choose notification settings - Notification Center and Alert Style (Off and None, I assume). Then choose "New Mail Sound". Select the New Mail Sound and Select the Vibration (None and None, I assume).
You can't do that, but you can set the Mail account you don't need to be notified to only fetch new mail when you open the app.
Go to Settings > Mail, Contacts, Calendars > Fetch New Data > Advanced
and change the schedule to Manual.